Mast cells (MCs) are versatile, multifunctional immune cells with broad roles in physiological homeostasis and pathogenic processes. MCs are found in most tissues, including skin, lungs, intestines, and peritoneum, and they vary in numbers, types, and biological functions. MCs are implicated in host defense against various pathogens, including bacteria, viruses, and fungi. Additionally, MCs are crucial in protecting against toxins, including those present in venoms from multiple species, such as honeybees, snakes, scorpions, and lizards. Although MCs play an essential role in host defense, they are mostly known for their detrimental actions in allergic reactions, such as asthma, food allergy, anaphylaxis, mastocytosis, and various inflammatory skin conditions. Under such conditions, MCs are activated (via IgE-mediated or other mechanisms) and release a range of potent proinflammatory mediators, including tumor necrosis factor α. In addition to cytokines, they are major producers of histamine and various proteases, including chymase, tryptase, and carboxypeptidase A3. As a result, these mediators contribute to the pathological manifestations associated with inflammatory conditions and other disorders. This review focuses mainly on the biological role of MCs and their proteases, with a focus on chymase and tryptase, as well as their inhibitors as candidate therapies for MC-driven diseases. Significance Statement Mast cells (MCs) and their proteases are central regulators of tissue homeostasis, barrier defense, and inflammation across multiple organs, but are also associated with numerous diseases. Ongoing research has shown that the function of MCs is highly dependent on their tissue location, where the local tissue environment shapes their phenotype, protease expression, and, consequently, their biological functions. However, further investigation is required to more precisely understand the physiological conditions governing the transition of MCs from maintaining tissue homeostasis to acquiring pathogenic functions, particularly with respect to their protease-dependent activities. By profiling MC heterogeneity using multiomics approaches to map protease-driven signaling networks, it will be possible to gain deeper insight into their functional roles and establish a conceptual framework to guide the development of next-generation, mechanism-based therapeutics that selectively modulate MC activity in human diseases.

Abstract Cathepsin C (CatC) is known to activate neutrophil serine proteases (NSPs) involved in innate immune function, although its broader impact on cellular proteolytic networks remains poorly defined. Here, we characterized the proteolytic landscape of HL-60 neutrophil progenitor cells following treatment with the CatC inhibitor brensocatib. Activity-based probes confirmed sustained inhibition of CatC by brensocatib, accompanied by progressive suppression of downstream elastase-like protease activation over 16 hours, 72 hours, and 7 days. An enrichment-free N-terminomics workflow was used to compare control and brensocatib-treated HL-60 cells. Following prolonged CatC inhibition, NSPs were reduced in abundance, while lysosomal cathepsins and endogenous protease inhibitors increased. These findings are consistent with remodeling of the protease-antiprotease network. Cleavage site analysis identified a pronounced, time-dependent, NSP-associated P1 cleavage signature enriched for Val, Thr, Ala, Ile, and Cys in control cells that was progressively lost following brensocatib treatment. We also identified established and candidate CatC-dependent cleavage events, together with proteolytic adaptations that emerged in the absence of CatC activity. Collectively, these findings demonstrate that CatC inhibition extends beyond suppression of canonical NSP activation to progressive remodeling of the broader protease-antiprotease network, providing new mechanistic insight into the cellular consequences of therapeutic CatC inhibition. Graphical Abstract

Abdominal pain is a debilitating symptom of inflammatory bowel disease (IBD). Despite advances in understanding IBD pathology, the mechanisms underlying pain remain poorly defined. While studies of tissue biopsies from IBD patients and rodent models have highlighted the roles of proinflammatory cytokines and proteases in pain signaling, these approaches predominantly capture host-derived mediators, overlooking the broader luminal environment influenced by the microbiota. Given the compromised barrier in IBD leading to increased mucosal permeability, examining the luminal milieu would characterize a novel source of factors involved in pain modulation in IBD patients with active disease. Fecal supernatants (FS) from healthy volunteers (HV) of either sex had no effect on ex vivo colonic afferent nerve mechanosensitivity or in vitro dorsal root ganglia (DRG) neuron excitability. In contrast, FS from Crohn's disease (CD) and ulcerative colitis (UC) patients of either sex significantly excited colonic afferent nerves and increased mechanosensitivity ex vivo and increased DRG neuronal excitability in vitro. These were blocked by the serine protease inhibitor and a protease-activated receptor 2 (PAR2) antagonist. Proteomic analysis revealed IBD FS contained elevated levels of trypsin-and elastase-like serine proteases compared with HV FS. Proteomics identified CELA3B, ELA2A, and PRSS1 as key proteases enriched in IBD FS, with distinct activity profiles in UC and CD. These findings establish that proteases within FS from IBD patients directly modulate pain-sensing pathways by activation of PAR2 on colonic afferent nerves, offering a unique insight into luminal contributions to pain and identifying potential therapeutic targets for visceral hypersensitivity in IBD.

Proteases contribute to essential cellular processes through catalyzing proteolysis, resulting in peptide bond hydrolysis and the generation of novel polypeptide species. Identification of proteolytic cleavage events is crucial for discerning proteolytic networks in biological systems, including the contribution of individual proteases to specific disease states. As such, various mass spectrometry-based workflows have been exploited for the sensitive identification of cleavage sites. To date, a range of enrichment strategies have been developed, focusing on increasing sensitivity, ease, and throughput for protease substrate discovery. Recent advances in mass spectrometry instrumentation have also permitted enrichment-free workflows for degradomics analysis, providing simultaneous and systematic assessment of the proteome and degradome. In this review, we discuss current technologies for the enrichment and identification of both N- and C-termini, as well as their application to profile protease specificity and decipher individual substrate repertoires in diverse biological conditions.

On-bead single-pot solid-phase enhanced sample preparation, SP3, also known as protein aggregation capture (PAC), is a robust, high-throughput, and widely utilized approach for proteomic sample preparation. Recent studies have highlighted PAC/SP3 as an ideal platform for chemoproteomics, allowing chemical labeling while minimizing sample loss and improving recovery of derivatized peptides. In this work, we establish an on-bead PAC/SP3 protein-level amine and carboxyl derivatization approach to facilitate C-terminal focused proteomics. We demonstrate that on-bead protein derivatization of carboxyl groups can be achieved using ethanolamine, (2-aminoethyl)trimethylammonium (AETMA), and (carboxymethyl)trimethylammonium (Girard's reagent T, GT) via EDC/HOBt coupling, enabling the labeling of protein C-termini. Using a prokaryotic model, Acinetobacter baumannii, we demonstrate that AETMA and ethanolamine labeling both enable identification of discrete protein C-terminal peptides, with AETMA enabling the detection of unique C-terminal peptides that lack basic residues. Finally, we apply this approach to interrogate both N- and C-termini in response to etoposide-induced apoptosis within Jurkat cells, demonstrating that combined N- and C-terminomics is achievable using on-bead derivatization, yet provides modest coverage of the C-terminome in its current form. Overall, this work establishes bead-based carboxyl group derivatization as a platform to enable future C-terminomics method development.

Avoiding lysosomal degradation is vital to the success of intracellular pathogens. The Gram-negative bacterium Coxiella burnetii and protozoan parasites of the Leishmania genus are unique in being able to replicate within the mature phagolysosomal compartment of host cells, though the exact mechanisms utilized to withstand this hostile environment are not clearly defined. We recently reported that C. burnetii removes the lysosomal protease cathepsin B during infection of mammalian cells. Here, we aimed to determine if this virulence strategy was also employed by the intralysosomal pathogen, Leishmania mexicana. In contrast to C. burnetii, decreases in the activity of specific cathepsins were not detected in L. mexicana-infected host cells as determined using immunoblotting and protease activity-based probes. Co-infection of THP-1 macrophage-like cells with both pathogens resulted in a proteolytic and secretory phenotype consistent with C. burnetii infection, suggesting that C. burnetii-induced remodeling of the lysosome is not influenced by L. mexicana. The host cell proteome and secretome of L. mexicana-infected cells were defined using mass spectrometry. This confirmed that, unlike C. burnetii, L. mexicana does not induce increased abundance of lysosomal proteins either intracellularly or in the extracellular milieu. Collectively, this study reveals that although C. burnetii and L. mexicana reside in a phagolysosomal intracellular niche, they employ divergent mechanisms to survive within this hostile compartment.

Cathepsin S is a cysteine protease that has been implicated in inflammatory bowel diseases (IBD) for its ability to promote visceral pain. Given its pro-inflammatory roles, we hypothesized that cathepsin S would drive other symptoms associated with IBD. Using activity-based probes, we investigated cysteine cathepsin activation in human and murine colitis. We observed a significant increase in fecal cathepsin S in patients with ulcerative colitis compared to healthy controls, while cathepsin S in mucosal biopsies was unchanged. Mice with experimental colitis exhibited a modest increase in mucosal activity of both cathepsin S and X compared to naïve mice. Luminal secretion of cathepsin S was dramatically increased upon colitis induction, although differences between mouse colonies were observed. To investigate the contribution of cathepsin S and cathepsin X to colitis, we induced colitis in cathepsin-deficient mice. Cathepsin X-deficient mice exhibited no clear differences in disease indicators compared to wild-type mice. While cathepsin S-deficient mice exhibited less rectal bleeding, less splenomegaly and marginally improved histological scores, weight loss, diarrhea, colon shortening, and myeloperoxidase activity were not significantly different from wild-type mice. To determine whether pharmacologic inhibition of cathepsin S activity would ameliorate symptoms of colitis, a reversible inhibitor LY3000328 was administered to mice at the initiation of colitis. LY3000328 provoked a clear upregulation of cathepsin S and L activity in the mucosa, most likely through a compensatory mechanism. This increase in protease activity was associated with exacerbated histological scores and slight splenomegaly. Collectively, these results suggest that cathepsin S, but not cathepsin X, may contribute to some of the symptoms of experimental colitis. While cathepsin S has potential to be a therapeutic target in colitis, improved strategies to sustain its inhibition are required in future.

Lysosomal proteases such as the cathepsin family and the asparaginyl endopeptidase, legumain, govern vital processes to maintain cellular proteostasis, and their dysregulation contributes to diverse pathologies. Recent studies have reported extra-lysosomal localisation of these proteases, especially in the nucleus, cytoplasm, and extracellularly, yet their function is not completely understood. To examine the relationship between legumain and cathepsins, we assessed the activity and expression of cathepsins in wild-type and legumain-deficient ( LGMN−/− ) cells using chemical activity-based probes and immunoblots. Processing of cathepsins (CTS) L, V, B, and D from the single-chain to the two-chain form was abrogated in the absence of legumain, with some cell type– and species-specific variation observed. This processing was dependent on legumain activity, although the mechanism remains unclear since recombinant legumain does not appear to directly cleave cathepsins in vitro . In cell types where CTSL exists in the nucleus preferentially in its double chain form, loss of legumain led to a reduction in nuclear CTSL levels. To understand the potential role of these lysosomal proteases in the nucleus, we applied our newly refined chemical N-terminomics pipeline, No-enrichment Identification of Cleavage Events (NICE). This analysis revealed widespread changes in both protein abundance and proteolysis, including putative nuclear substrates of CTSL and legumain, that primarily suggest roles in cell proliferation, cell cycle regulation, inflammation, and ribosomal biogenesis. Overall, this study builds on our understanding of the relationship between legumain and cathepsins and provides the first systematic characterisation of lysosomal protease substrates in the nucleus. Our results offer valuable insight into the potential extra-lysosomal roles of these critical proteases. ### Competing Interest Statement The authors have declared no competing interest. * ABP : activity-based probe AEP : asparaginyl endopeptidase BCA : bicinchoninic acid CM : conditioned media CTS : cathepsin CTSB : cathepsin B CTSC : cathepsin C CTSD : cathepsin D CTSH : cathepsin H CTSL : cathepsin L CTSL−/− : cathepsin L knockout CTSS : cathepsin S CTSV : cathepsin V CTSX : cathepsin X/Z CUX1 : CCAAT-displacement protein/cut homeobox transcription factor 1 DC : double-chain DIA : data-independent acquisition ECM : extracellular matrix EGFR : epithelial growth factor receptor EMT : epithelial-to-mesenchymal transition FAIMS : high-field asymmetric waveform ion mobility spectrometry GO : gene ontology GRN : progranulin HSNCC : head and neck squamous cell carcinoma ICE : inference of CRISPR edits IL : interleukin LGMN : legumain LGMN−/− : legumain knockout LMP : lysosomal membrane permeability M6P : mannose-6-phosphate MMP2 : matrix metalloprotease 2 NICE : no-enrichment identification of cleavage events NLS : nuclear localisation signal PTM : post-translational modification SC : single-chain STAT : signal transducer and activator of transcription TGFB : transforming growth factor beta TLR : toll-like receptor TME : tumour microenvironment TNF-α : tumour necrosis factor alpha TPG : trypsinogen WT : wild-type National Health and Medical Research Council, https://ror.org/011kf5r70, 2011119, 2018980 Australian Research Council, DE180100418, FT200100270, DP210100362 Russell and Mab Grimwade Miegunyah Fund

Aberrant levels of the cysteine protease Calpain-2 have been linked to neurodegeneration, inflammation, and cancer, yet our understanding of this protease and its substrates remains limited. Systematic studies to identify Calpain-2 substrates have been largely confined to peptide libraries or in vitro studies, which fail to represent physiological cellular conditions and physiologically relevant substrates. To identify existing and novel Calpain-2 substrates, we used a genetic approach to knockout Calpain-2 in the THP-1 human monocyte-like cells, followed by proteomic and N-terminomic/TAILS mass spectrometry approaches to identify Calpain-2 substrates. We identified 51 substrates that may be cleaved directly by Calpain-2 or indirectly by downstream proteases. The direct cleavage of selected substrates by Calpain-2 was confirmed using in vitro assays. Finally, metabolomics analysis identified a role for Calpain-2 in the regulation of pyrimidine and glutathione metabolism. Our unbiased and quantitative mass spectrometry analytical pipeline provides new evidence on the physiological functions of Calpain-2 and its newly identified substrates in THP-1 cells.

The obligate intracellular bacterium Coxiella burnetii establishes an intracellular replicative niche termed the Coxiella-containing vacuole (CCV), which has been characterised as a bacterially modified phagolysosome. How C. burnetii withstands the acidic and degradative properties of this compartment is not well understood. We demonstrate that the key lysosomal protease cathepsin B is actively and selectively removed from C. burnetii-infected cells through a mechanism involving the Dot/Icm type IV-B secretion system effector CvpB. Overexpression of cathepsin B leads to defects in CCV biogenesis and bacterial replication, indicating that removal of this protein represents a strategy to reduce the hostility of the intracellular niche. In addition, we show that C. burnetii infection of mammalian cells induces the secretion of a wider cohort of lysosomal proteins, including cathepsin B, to the extracellular milieu via a mechanism dependent on retrograde traffic. This study reveals that C. burnetii is actively modulating the hydrolase cohort of its replicative niche to promote intracellular success and demonstrates that infection incites the secretory pathway to maintain lysosomal homoeostasis.

The mammalian lysosomal protease legumain is often dysregulated in pathophysiological conditions including inflammation, neurodegeneration, and cancer, yet its proteolytic targets are poorly defined. To profile protease substrates, degradomics techniques typically employ enrichment strategies to select for sub-stoichiometric and low-abundance peptides generated by proteolytic cleavage. However, recent advancements in degradomics techniques have revealed N-termini enrichment can be circumvented if peptide-based fractionation is employed, enabling simultaneous proteome and N-terminome analysis. Herein, we compare the previously published enrichment-free N-terminomics approach using high-field asymmetric waveform ion mobility spectrometry (FAIMS) to offline basic reverse-phase (bRP) fractionation to assess the complementarity of these fractionation methods for simultaneous proteomic and degradomic analyses. While at the protein level FAIMS and bRP provide access to overlapping proteomic coverage, at the N-terminus level each fractionation technique reveals unique cleavage information. Combining data from the two fractionation approaches revealed 6499 N-terminal peptides with N-terminal TMTpro labeling, allowing the identification of cleavage events modulated in the context of legumain deficiency in naïve murine colons and during dextran sulfate sodium (DSS)-induced colitis. Among these N-termini, we identify 35 putative legumain substrates in naïve and 41 in the DSS-treated colons, supporting a role for legumain in both pro-inflammatory and physiological conditions. Use of an additional negative selection method, High-efficiency Undecanal-based N-Termini EnRichment (HUNTER), further supplements this list of identified legumain substrates. Combined, this study identifies multiple putative substrates of legumain in healthy and inflamed murine colons as well as demonstrates the utility of using complementary fractionation approaches for degradomics studies.

While the cysteine proteases legumain and cathepsins have traditionally been known as "lysosomal" proteases, there is increasing evidence to suggest that they also contribute to a wide range of extralysosomal processes, including in the nucleus. This review aims to provide a comprehensive overview of the current knowledge regarding the translocation of these proteases to the nucleus and their functions on arrival. We discuss possible mechanisms for transporting these proteases to the nucleus, including the presence of a nuclear localization signal sequence or hitchhiking on other proteins that possess this sequence. This transport requires the proteases to first reach the cytosol, which may occur via direct cytosolic translation of truncated proteases or downstream of lysosomal membrane permeabilization. We also discuss the evidence for functions of these proteases upon arrival to the nucleus, including cell cycle progression, cell differentiation, cell death, immune regulation, and epigenetic regulation. As protease substrate profiling methods continue to improve, it is anticipated that many new nuclear substrates and interacting partners will be identified to reveal additional functions for nuclear proteases.

Dendritic cells (DCs) are professional antigen-presenting cells endowed with the capacity to initiate strong antitumor immune responses. This function is critical for effective DC-based immunotherapies but is often hampered by tumor-derived immunosuppressive factors, as is observed for CD14+CD163+ tumor-induced DC3s (ti-DC3s). ti-DC3s are increased in cancer patients where they display an immunosuppressive phenotype, accompanied by weak antigen-specific CD8 T cell-activating capacities. While tumor-derived interleukin-6, macrophage colony-stimulating factor, and prostaglandin E2 have been identified as factors inducing the transition from DC2s to ti-DC3s, a comprehensive unbiased profiling of the resulting changes in secretome and proteome has not been reported. Here, we characterized by tandem LC-MS/MS the proteomic changes in conventional DCs during their transition into CD14+ ti-DC3s in vitro, using conditioned medium from the melanoma cell line BLM. This revealed 157 differentially expressed proteins, including upregulated indoleamine-2,3-dioxygenase 1 and legumain, which we confirmed to be functionally active. Next, we profiled the newly synthesized secretome in human DCs with THRONCAT metabolic labeling. We detected 17 differentially secreted proteins between DC2s and ti-DC3s, which included six cathepsins and tumor-associated transforming growth factor-β-induced protein. Cathepsin activity was validated in peripheral blood and tumor tissue of melanoma patients. We detected the highest cathepsin activity in ti-DC3s, surpassing DC2s and tumor-associated macrophages. Together, our findings represent the first characterization of the proteome and secretome of human melanoma-induced DC3s. This revealed several protein-driven protumor mechanisms active in ti-DC3s that potentially contribute to creating an immune environment favorable for tumor progression.

Aberrant levels of the asparaginyl endopeptidase legumain have been linked to inflammation, neurodegeneration and cancer, yet our understanding of this protease is incomplete. Systematic attempts to identify legumain substrates have previously been confined to in vitro studies, which fail to mirror physiological conditions and obscure biologically relevant cleavage events. Using high-field asymmetric waveform ion mobility spectrometry (FAIMS), we developed a sensitive and streamlined approach for proteome and N-terminome analyses in a single analytical method without the need for N-termini enrichment. Compared to unfractionated proteomic analysis, we demonstrate FAIMS fractionation improves neo-N- termini identification by >2.5 fold, resulting in identification of >2,882 unique neo-N-termini from limited sample amounts. Within murine spleens, this approach identifies 6,366 proteins and 2,528 unique neo-N-termini, with 235 cleavage events enriched in wild-type compared to legumain-deficient spleens. Among these, 119 neo-N-termini arose from asparaginyl endopeptidase activities, representing novel putative physiological legumain substrates. The direct cleavage of selected substrates by legumain was confirmed using in vitro assays, providing support for the existence of physiologically relevant extra-lysosomal legumain activity. Combined, these data shed critical light on the functions of legumain and demonstrates the utility of FAIMS as an accessible method to improve depth and quality of N- terminomics studies.

Human norovirus is the leading cause of acute gastroenteritis worldwide, however despite the significance of this pathogen, we have a limited understanding of how noroviruses cause disease, and modulate the innate immune response. Programmed cell death (PCD) is an important part of the innate response to invading pathogens, but little is known about how specific PCD pathways contribute to norovirus replication. Here, we reveal that murine norovirus (MNV) virus-induced PCD in macrophages correlates with the release of infectious virus. We subsequently show, genetically and chemically, that MNV-induced cell death and viral replication occurs independent of the activity of inflammatory mediators. Further analysis revealed that MNV infection promotes the cleavage of apoptotic caspase-3 and PARP. Correspondingly, pan-caspase inhibition, or BAX and BAK deficiency, perturbed viral replication rates and delayed virus release and cell death. These results provide new insights into how MNV harnesses cell death to increase viral burden.

Cysteine cathepsins are lysosomal proteases subject to dynamic regulation within antigen-presenting cells during the immune response and associated diseases. To investigate the regulation of cathepsin X, a carboxy-mono-exopeptidase, during maturation of dendritic cells (DCs), we exposed immortalized mouse DCs to various Toll-like receptor agonists. Using a cathepsin X-selective activity-based probe, sCy5-Nle-SY, we observed a significant increase in cathepsin X activation upon TLR-9 agonism with CpG, and to a lesser extent with Pam3 (TLR1/2), FSL-1 (TLR2/6) and LPS (TLR4). Despite clear maturation of DCs in response to Poly I:C (TLR3), cathepsin X activity was only slightly increased by this agonist, suggesting differential regulation of cathepsin X downstream of TLR activation. We demonstrated that cathepsin X was upregulated at the transcriptional level in response to CpG. This occurred at late time points and was not dampened by NF-kappa B inhibition. Factors secreted from CpG-treated cells were able to provoke cathepsin X upregulation when applied to na & iuml;ve cells. Among these factors was IL-6, which on its own was sufficient to induce transcriptional upregulation and activation of cathepsin X. IL-6 is highly secreted by DCs in response to CpG but much less so in response to poly I:C, and inhibition of the IL-6 receptor subunit glycoprotein 130 prevented CpG-mediated cathepsin X upregulation. Collectively, these results demonstrate that cathepsin X is differentially transcribed during DC maturation in response to diverse stimuli, and that secreted IL-6 is critical for its dynamic regulation. Cathepsin X is a lysosomal cysteine protease known to impact dendritic cell function. We demonstrate that its expression and activity are dynamically regulated during the maturation of dendritic cells in response to TLR agonism, and that transcriptional upregulation of cathepsin X is mediated by secreted IL-6. image

Covalent activity-based probes are invaluable tools to monitor protease activity in vitro and in vivo. We recently discovered that dimethyl sulfoxonium ylides (SYs) bind selectively to cysteine cathepsin proteases in a mechanism-dependent manner. Herein, we present the synthetic routes and characterization of an expanded library of SY probes with a greater diversity in recognition sequences. The probes exhibit a range of potency and selectivity for the cathepsin family members. We also investigated the impact of fluorophore positioning on probes bearing P1 lysine. When sulfonated cyanine 5 was attached via the lysine side chain, the resulting probe was selective for cathepsin S. When attached to the alpha-amine, with the side chain amine either free or Boc-protected, the probes reacted with both cathepsin S and X. Bulk in the P1 position is thus well tolerated by cathepsin S but not cathepsin X. We examined the impact of Cy5 sulfonation on probe properties, demonstrating that unsulfonated probes exhibit greater cellular uptake, which affects their relative selectivity. Finally, we demonstrated that SY probes exhibit minimal labeling of cathepsin S in freshly prepared lysates, but this increases during the prolonged incubation of lysates. This work extends our understanding of SY probes and informs future probe development.

Proteases function within sophisticated networks. Altering the activity of one protease can have sweeping effects on other proteases, leading to changes in their activity, structure, specificity, localisation, stability, and expression. Using a suite of chemical tools, we investigated the impact of cathepsin X, a lysosomal cysteine protease, on the activity and expression of other cysteine proteases and their inhibitors in dendritic cells. Among all proteases examined, cathepsin X gene deletion specifically altered cathepsin L levels; pro-cathepsin L and its single chain accumulated while the two-chain form was unchanged. This effect was recapitulated by chemical inhibition of cathepsin X, suggesting a dependence on its catalytic activity. We demonstrated that accumulation of pro- and single chain cathepsin L was not due to a lack of direct cleavage by cathepsin X or altered glycosylation, secretion, or mRNA expression but may result from changes in lysosomal oxidative stress or pH. In the absence of active cathepsin X, nuclear cathepsin L and cleavage of the known nuclear cathepsin L substrate, Lamin B1, were diminished. Thus, cathepsin X activity selectively regulates cathepsin L, which has the potential to impact the degree of cathepsin L proteolysis, the nature of substrates that it cleaves, and the location of cleavage.

Legumain is a cysteine protease broadly associated with inflammation. It has been reported to cleave and activate protease-activated receptor 2 to provoke pain associated with oral cancer. Outside of gastric and colon cancer, little has been reported on the roles of legumain within the gastrointestinal tract. Using a legumain-selective activity-based probe, LE28, we report that legumain is activated within colonocytes and macrophages of the murine colon, and that it is upregulated in models of acute experimental colitis. We demonstrated that loss of legumain activity in colonocytes, either through pharmacological inhibition or gene deletion, had no impact on epithelial permeability in vitro. Moreover, legumain inhibition or deletion had no obvious impacts on symptoms or histological features associated with dextran sulfate sodium-induced colitis, suggesting its proteolytic activity is dispensable for colitis initiation. To gain insight into potential functions of legumain within the colon, we performed field asymmetric waveform ion mobility spectrometry-facilitated quantitative proteomics and N-terminomics analyses on naïve and inflamed colon tissue from wild-type and legumain-deficient mice. We identified 16 altered cleavage sites with an asparaginyl endopeptidase signature that may be direct substrates of legumain and a further 16 cleavage sites that may be indirectly mediated by legumain. We also analyzed changes in protein abundance and proteolytic events broadly associated with colitis in the gut, which permitted comparison to recent analyses on mucosal biopsies from patients with inflammatory bowel disease. Collectively, these results shed light on potential functions of legumain and highlight its potential roles in the transition from inflammation to colorectal cancer.